Let me take a shot at explaining this:
The reason water gets sucked into the engine is because there is no "pump" that circulates water to cool the exhaust (and supercharger, if you have it). There are holes in the venturi that bleed water off when the impeller is pushing water through the jet pump. That force of water through the jet pump that propels the boat is also the pressure that forces some of that water up to the exhaust to cool it. When the engine is running, the exhaust gasses force that cooling water back out the exhaust port after it has completed the cooling loop.
When the engine is not running and the boat is sitting still, there is no pressure on the venturi to force water into the exhaust cooling loop - so, no problem with water entering the block. When you are getting towed, there is some water pressure (depending on speed) on the venturi, causing water to flow into the exhaust cooling loop. Once the loop fills up, it spills over into the exhaust. Once the exhaust fills up (remember, there is no exhaust gas pressure on the exhaust system to force water out of the exhaust outlet), water flows up to the head of the engine and sits there. When you crank the engine and the valves open, water falls into the cylinders and you get hydrolock.
This is why you can tow the boat at a low speed without a problem, but if you exceed the threshold where the venturi comes under pressure, you WILL fill the engine with water.
Clamping or valving off the venturi hose to the manifold will allow you to tow the boat at a faster speed and not fill the engine because the water under pressure in the venturi has nowhere to go.